LAMMPS (18 Feb 2013)
# Rhodopsin model

newton off
package 	gpu force/neigh 0 1 1

variable	x index 2
variable	y index 2
variable	z index 2

units           real
neigh_modify    delay 5 every 1

atom_style      full
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
pair_style      lj/charmm/coul/long/gpu 8.0 10.0
pair_modify     mix arithmetic
kspace_style    pppm/gpu 1e-4

read_data       data.rhodo
  4 = max bonds/atom
  18 = max angles/atom
  40 = max dihedrals/atom
  4 = max impropers/atom
  orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
  1 by 2 by 2 MPI processor grid
  32000 atoms
  32000 velocities
  27723 bonds
  40467 angles
  56829 dihedrals
  1034 impropers
  4 = max # of 1-2 neighbors
  12 = max # of 1-3 neighbors
  24 = max # of 1-4 neighbors
  26 = max # of special neighbors

replicate	$x $y $z
replicate	2 $y $z
replicate	2 2 $z
replicate	2 2 2
  orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
  1 by 2 by 2 MPI processor grid
  256000 atoms
  221784 bonds
  323736 angles
  454632 dihedrals
  8272 impropers
  4 = max # of 1-2 neighbors
  12 = max # of 1-3 neighbors
  24 = max # of 1-4 neighbors
  26 = max # of special neighbors

fix             1 all shake 0.0001 5 0 m 1.0 a 232
  12936 = # of size 2 clusters
  29064 = # of size 3 clusters
  5976 = # of size 4 clusters
  33864 = # of frozen angles
fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1

special_bonds   charmm

thermo          100
thermo_style    multi
timestep        2.0

run		200
PPPM initialization ...
  G vector (1/distance) = 0.245959
  grid = 48 64 60
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0410392
  estimated relative force accuracy = 0.000123588
  using double precision FFTs
  3d grid and FFT values/proc = 68635 46080
Memory usage per processor = 250.358 Mbytes
---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
TotEng   =    157024.0492 KinEng   =    172792.6155 Temp     =       301.1796 
PotEng   =    -15768.5663 E_bond   =     28164.9917 E_angle  =    117224.0742 
E_dihed  =     61174.8491 E_impro  =      3752.0273 E_vdwl   =     10108.6324 
E_coul   =   1894295.6622 E_long   =  -2130488.8032 Press    =      9562.1554 
Volume   =   2457390.7959 
---------------- Step      100 ----- CPU =     12.1280 (sec) ----------------
TotEng   =   -233301.6590 KinEng   =    123222.8183 Temp     =       214.7789 
PotEng   =   -356524.4772 E_bond   =     13098.4683 E_angle  =     56766.9228 
E_dihed  =     45556.8211 E_impro  =      1313.9369 E_vdwl   =    -40863.9000 
E_coul   =   1705084.8591 E_long   =  -2137481.5855 Press    =     -1634.3808 
Volume   =   2522232.6313 
---------------- Step      200 ----- CPU =     23.3169 (sec) ----------------
TotEng   =   -308342.2597 KinEng   =    108936.8553 Temp     =       189.8783 
PotEng   =   -417279.1150 E_bond   =      9579.0042 E_angle  =     47373.6037 
E_dihed  =     39847.3737 E_impro  =       967.6451 E_vdwl   =    -23631.6382 
E_coul   =   1646630.1738 E_long   =  -2138045.2773 Press    =     -1185.5491 
Volume   =   2554682.9808 
Loop time of 23.3169 on 4 procs for 200 steps with 256000 atoms

Pair  time (%) = 4.29395 (18.4156)
Bond  time (%) = 6.57406 (28.1944)
Kspce time (%) = 4.75311 (20.3848)
Neigh time (%) = 1.32057 (5.66359)
Comm  time (%) = 0.555436 (2.38212)
Outpt time (%) = 0.000431776 (0.00185177)
Other time (%) = 5.81936 (24.9577)

FFT time (% of Kspce) = 1.78333 (37.5192)
FFT Gflps 3d (1d only) = 5.0126 11.639

Nlocal:    64000 ave 64003 max 63997 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost:    70636.8 ave 70640 max 70632 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs:    0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 7.43187
Neighbor list builds = 31
Dangerous builds = 12
